Leishmaniasis is a serious public health concern in the Northeastern region of Brazil, where the sand fly fauna is well studied, although few species have been identified as competent vectors. The detection of Leishmania spp. parasites in wild-caught sand flies could help sanitary authorities draw strategies to avoid the transmission of the parasites and, therefore, the incidence of leishmaniases. We detected Leishmania DNA in wild-caught sand flies and correlated that data with aspects of sand fly ecology in the Caxias municipality, Maranhao State, Brazil. The sand flies were sampled in the peridomicile (open areas in the vicinity of human residences) and intradomicile (inside the residences) from July/2019 to March/2020. Leishmania DNA was detected in females, targeting a fragment of the Internal Transcribed Spacer (ITS1) from ribosomal DNA. Among the fourteen species of sand flies identified, five (Lutzomyia longipalpis, Nyssomyia whitmani, Evandromyia evandroi, Micropygomyia trinidadensis, and Micropygomyia quinquefer) harbored DNA of Leishmania (Leishmania) amazonensis. The most abundant species in rural (Ny. whitmani: 35.2% and Ev. evandroi: 32.4%) and urban areas (Lu. longipalpis: 89.8%) are the permissive vectors of L. (L.) amazonensis, especially Ny. whitmani, a known vector of causative agents of cutaneous leishmaniasis. Although Lu. longipalpis is the vector of L. (L.) infantum, which was not detected in this study, its permissiveness for the transmission of L. (L.) amazonensis has been reported. We suspect that visceral leishmaniasis and cutaneous leishmaniasis are caused by L. (L.) amazonensis, and the transmission may be occurring through Lu. longipalpis, at least in the urban area.